Interaction of SARS-CoV-2 with host cells and antibodies: experiment and simulation

H Nguyen, HL Nguyen, PD Lan, NQ Thai… - Chemical Society …, 2023 - pubs.rsc.org
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of
the devastating global COVID-19 pandemic announced by WHO in March 2020. Through …

High-speed atomic force microscopy for filming protein molecules in dynamic action

T Ando, S Fukuda, KX Ngo… - Annual Review of …, 2023 - annualreviews.org
Structural biology is currently undergoing a transformation into dynamic structural biology,
which reveals the dynamic structure of proteins during their functional activity to better …

Single-molecule force stability of the SARS-CoV-2–ACE2 interface in variants-of-concern

MS Bauer, S Gruber, A Hausch, MCR Melo… - Nature …, 2024 - nature.com
Mutations in SARS-CoV-2 have shown effective evasion of population immunity and
increased affinity to the cellular receptor angiotensin-converting enzyme 2 (ACE2) …

Probing conformational landscapes of binding and allostery in the SARS-CoV-2 omicron variant complexes using microsecond atomistic simulations and perturbation …

G Verkhivker, M Alshahrani, G Gupta, S Xiao… - Physical Chemistry …, 2023 - pubs.rsc.org
In this study, we systematically examine the conformational dynamics, binding and allosteric
communications in the Omicron BA. 1, BA. 2, BA. 3 and BA. 4/BA. 5 spike protein complexes …

Coarse-Grained Molecular Simulations and Ensemble-Based Mutational Profiling of Protein Stability in the Different Functional Forms of the SARS-CoV-2 Spike …

G Verkhivker, M Alshahrani, G Gupta - International Journal of Molecular …, 2023 - mdpi.com
Evolutionary and functional studies have suggested that the emergence of Omicron variants
can be determined by multiple fitness tradeoffs including immune escape, binding affinity …

[HTML][HTML] Atomic force microscopy as a nanolithography tool to investigate the DNA/gold interface

P Canepa, SMC Rotondi, O Cavalleri - Current Opinion in Electrochemistry, 2024 - Elsevier
This concise survey delves into the capabilities of atomic force microscopy (AFM) for
investigating the DNA/gold interface. It highlights how the precise control of the force applied …

Biophysical investigation of interactions between SARS‐CoV‐2 spike protein and neuropilin‐1

D Hou, W Cao, S Kim, X Cui, M Ziarnik, W Im… - Protein …, 2023 - Wiley Online Library
Recent studies have suggested that neuropilin‐1 (NRP1) may serve as a potential receptor
in severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection. However, the …

Single-Molecule Investigation of the Binding Interface Stability of SARS-CoV-2 Variants with ACE2

A Ray, TT Minh Tran, R Santos Natividade… - ACS Nanoscience …, 2024 - ACS Publications
The SARS-CoV-2 pandemic spurred numerous research endeavors to comprehend the
virus and mitigate its global severity. Understanding the binding interface between the virus …

Molecular Recognition in Confined Space Elucidated with DNA Nanopores and Single-Molecule Force Microscopy

SH Suh, Y Xing, A Rottensteiner, R Zhu, YJ Oh… - Nano Letters, 2023 - ACS Publications
The binding of ligands to receptors within a nanoscale small space is relevant in biology,
biosensing, and affinity filtration. Binding in confinement can be studied with biological …

Structure-Guided Development of Bivalent Aptamers Blocking SARS-CoV-2 Infection

MS Rahman, MJ Han, SW Kim, SM Kang, BR Kim… - Molecules, 2023 - mdpi.com
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused devastation to
human society through its high virulence, infectivity, and genomic mutations, which reduced …